[2024-01-24 14:06:07,056] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference
[2024-01-24 14:06:08,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,411] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,411] [INFO] Running command: gunzip -c /var/lib/cwl/stgc51f3896-e876-45f1-a1e5-6e2e1e0366b4/GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/cds.fna -a GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,329] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,329] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,329] [INFO] Running command: hmmsearch --tblout GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/reference_markers.hmm GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,649] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,685] [INFO] Query marker FASTA was written to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:16,688] [INFO] Task started: Blastn
[2024-01-24 14:06:16,688] [INFO] Running command: blastn -query GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/reference_markers.fasta -out GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,713] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:17,714] [INFO] Target genome list was writen to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,727] [INFO] Task started: fastANI
[2024-01-24 14:06:17,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgc51f3896-e876-45f1-a1e5-6e2e1e0366b4/GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna.gz --refList GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:32,025] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:32,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:32,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:32,042] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:32,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:32,043] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	100.0	988	988	95	conclusive
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	84.2851	742	988	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	84.1005	692	988	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	83.8275	718	988	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	82.1904	604	988	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.0232	620	988	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	81.6651	578	988	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	81.6424	590	988	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.5464	557	988	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.9907	572	988	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.4337	561	988	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.0363	524	988	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.5449	344	988	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.3558	407	988	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	76.2437	134	988	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	76.2002	130	988	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.153	174	988	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	75.9824	169	988	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	75.9661	168	988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,045] [INFO] DFAST Taxonomy check result was written to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:32,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:32,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:32,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/checkm_data
[2024-01-24 14:06:32,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:32,088] [INFO] Task started: CheckM
[2024-01-24 14:06:32,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/checkm_input GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:00,901] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:00,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,923] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:00,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:00,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:00,925] [INFO] Task started: Blastn
[2024-01-24 14:07:00,925] [INFO] Running command: blastn -query GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3109b501-be1d-453b-b8eb-9a832134bf2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:02,591] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:02,595] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:02,596] [INFO] Target genome list was writen to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,609] [INFO] Task started: fastANI
[2024-01-24 14:07:02,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgc51f3896-e876-45f1-a1e5-6e2e1e0366b4/GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna.gz --refList GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:13,261] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:13,282] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:13,283] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900116065.1	s__Brevundimonas viscosa	100.0	988	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001794825.1	s__Brevundimonas sp001794825	91.037	824	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	88.575	782	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	85.1656	458	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	84.7295	671	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	84.2721	743	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202075.1	s__Brevundimonas basaltis	84.125	690	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	84.1079	716	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427825.1	s__Brevundimonas sp001427825	83.9498	700	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	83.812	719	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	83.6386	660	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204035.1	s__Brevundimonas diminuta	81.6737	577	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCF_001424025.1	s__Brevundimonas sp001424025	81.5285	600	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421705.1	s__Brevundimonas naejangsanensis	81.1041	568	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.43	97.43	0.89	0.89	2	-
GCF_015999335.1	s__Tabrizicola soli	76.1764	176	988	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,284] [INFO] GTDB search result was written to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:13,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:13,289] [INFO] DFAST_QC result json was written to GCF_900116065.1_IMG-taxon_2671180176_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:13,289] [INFO] DFAST_QC completed!
[2024-01-24 14:07:13,289] [INFO] Total running time: 0h1m6s